Approximating the coalescent with recombination

McVean, Gil; Cardin, Niall J.

doi:10.1098/rstb.2005.1673

Cited by 365 publications

(443 citation statements)

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“…Other approaches, such as diffusion approximations for demographic inference (@a@i) (Gutenkunst et al 2009), use the probability density of the site frequency spectrum (SFS) under a given demographic model and parameterization to calculate the likelihood of the observed SFS (Marth et al 2004;Gutenkunst et al 2009), thereby allowing for optimization of model parameters. More recently, methods based on the sequentially Markovian coalescent (SMC) (McVean and Cardin 2005;Marjoram and Wall 2006) have been devised (Li and Durbin 2011;Sheehan et al 2013;Schiffels and Durbin 2014), to infer how a population's size has changed over time through the description of patterns of genetic variation along a recombining chromosome.…”

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Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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The availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies, they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of data sets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models-often severely. We find that selection can lead to incorrect inferences of population size changes when none have occurred. Moreover, we show that linked selection can lead to incorrect demographic model selection, when multiple demographic scenarios are compared. We argue that natural populations may experience the amount of recent positive selection required to skew inferences. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.KEYWORDS population genetics; positive selection; demographic inference T HE widespread availability of population genomic data has spurred a new generation of studies aimed at understanding the histories of natural populations from a host of model and nonmodel organisms alike. In particular, genomescale variation data allows for inference of demographic factors such as population size changes, the timing and ordering of population splits, migration rates between populations, and the founding of admixed populations (Pool et al. 2010;Pickrell and Pritchard 2012;Sousa and Hey 2013). Such efforts can refine our picture of demographic events inferred from the archaeological record (e.g., Fagundes et al. 2007;Goebel et al. 2008), or reveal such events in species where no archaeological data are available, and can aid conservation efforts by complementing census data (e.g., Hájková et al. 2007;Garrick et al. 2015).Population genomic data sets are well suited for this task simply because demographic changes leave their mark on patterns of genetic variation. Recent population growth, for example, will result in an excess of rare variation compared to equilibrium expectations (Fu 1997), while population contraction will result in an excess of intermediate frequency alleles (Maruyama and Fuerst 198...

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Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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“…Apesar dessas informações serem relevantes para a realização de estudos de mapeamento associativo, é desejável obter uma visão do DL sob o ponto de vista genealógico (Nordborg and Tavaré, 2002;Zöllner and von Haeseler, 2000;McVean, 2002;McVean and Cardin, 2005;McVean, 2007a), considerando as possíveis relações evolutivas entre sequências de DNA. Nesse sentido, a teoria da coalescência, que realiza inferências do presente em direção ao passado (Hudson, 1990;Fu and Li, 1999;Wakeley, 2009), poder ser bastante útil para a caracterização do DL em painéis de associação, principalmente para espécies que possuem poucas informações de genealogias.…”

Section: Desequilíbrio De Ligaçãounclassified

“…Neste contexto, é fundamental saber aquilo que de fato está sendo estimado, pois, no primeiro o caso, µ é a taxa de mutação por geração, indivíduo e para cada sítio, enquanto que, no segundo caso, µ é a taxa de mutação por geração, indivíduo e região cromossômica (Fu and Li, 1999;Nordborg, 2007;Nordborg and Tavaré, 2002;Hein et al, 2004;McVean and Cardin, 2005;Wakeley, 2009). De qualquer forma, normalmente o interesse está no parâmetro θ, pois é muito difícil distinguir N e e µ a partir dos dados sem informações históricas prévias.…”

Section: Mutaçãounclassified

“…Assim, modelos de coalescência com recombinação tendem a ser mais complexos, algo que se torna ainda mais desafiador e intensivo pelo fato de que nenhuma configuração de genealogia pode ser trivialmente modelada diante deste cenário (Hein et al, 2004). Isso acontece porque um evento de recombinação é modelado de forma que uma única sequência mais recente é "quebrada" em posição aleatória para formar duas sequências mais antigas (Hein et al, 2004;McVean and Cardin, 2005;Nordborg, 2007), sendo o contrário de um evento de coalescência. Então, o processo evolutivo deste modelo é melhor representado por um gráfico e não por uma genealogia, tendo-se, portanto, tanto eventos de coalescência quanto eventos de recombinação (Hein et al, 2004;Nordborg, 2007).…”

Section: Recombinaçãounclassified

“…Por contemplar eventos de coalescência e recombinação modelados aleatoriamente no passado, Griffiths and Marjoram (1996) propuseram a nomenclatura "gráfico de recombinação ancestral" (ARG, do inglês Ancestral Recombination Graph) anos mais tarde. Como alternativa ao modelo de Hudson (1983), Wiuf and Hein (1999) desenvolveram uma forma de simular ARGs percorrendo as sequências amostradas de um lado para outro, caracterizando uma complexa estrutura não-Markoviana (McVean and Cardin, 2005). Embora este método tenha tido sua importância, a primeira abordagem é considerada mais simples e útil (Hein et al, 2004).…”

Section: Recombinaçãounclassified

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Análise da estrutura populacional e do desequilíbrio de ligação de um painel de acessos de sorgo: uma abordagem usando teoria da coalescência

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Inferring the Process of Human–Chimpanzee Speciation

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Although the fossil record around the times of the key speciation events that splits humans from orangutans, gorillas and chimpanzees is sparse, genetic comparisons of the extant apes enable us to analyse the process of speciation that lead to modern humans. Deoxyribonucleic acid (DNA) sequencing technology has improved greatly over the last decade and the complete genomes of all great apes have now been mapped. Analysis of this rich data has enabled the inference of key parameters of their speciation events. Though inference of the speciation events has so far focussed on simple models it is an active area of research to develop better models and understand the processes involved in the speciation and divergence of the great apes. Of the speciations along the human lineage, the split between ourselves and our closest living relatives, the chimpanzees and bonobos, naturally receives special attention. Key Concepts: Population genetics modelling of speciation events informs us of the timing and mode of ancient speciations from present day genomic data. A strong source of information about speciation is found in the changing gene trees along a genomic alignment. By studying great ape genomes we learn about the speciations along the human lineage, where the human–chimpanzee speciation is of special interest. It is still an open question if this speciation was a clean (allopatric) split or if occurred in the presence of gene flow or was followed by admixture events. If the speciation happened in the presence of gene flow it might have left signals of which genes first became incompatible and drove the speciation.

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Approximating the coalescent with recombination

Cited by 365 publications

References 29 publications

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Análise da estrutura populacional e do desequilíbrio de ligação de um painel de acessos de sorgo: uma abordagem usando teoria da coalescência

Inferring the Process of Human–Chimpanzee Speciation

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